Daily Status, Sept 28: Low numbers, even for a monday! Good to see.

 

Daily Status, Sept. 28

Reminder:  any sections that are unchanged since yesterday are grayed out.  

Situational Awareness

Today, Virginia has only 449 newly diagnosed COVID cases; this is the fewest number since around July 4. If we look at 7 day numbers, we have averaged 780 cases (9.3/100K), which is 3.3 standard deviations below the mean weekly number for the last 11 weeks;  This event has about a 1 in 1000 chance of happening randomly, so, it is probably significant:  our cases are declining (or the reporting is faulty).  Overall, cases are decreasing  for the last three week at 1.4%/day, or 10% a week.  There were 41 new cases associated with colleges, which is very low, but monday's tend to be lower at colleges (Health Centers are typically closed on Sundays).  This is the lowest number of cases since August 21 when the Radford  began.

Regionally, all districts showing are flat to negative case growth. The testing numbers now show the percent positive to be below the 5% metric that is often used to indicate sufficient testing (e.g., is is safe to reopen schools)..  On one other front, over the last week, we are below to the metric of 10 cases per 100,000 to enter states like NY without quarantine -- we are at 9.3 down from 12 or so a week ago.  If the numbers do not increase, we should be off NY's quarantine list soon.

Outside of a few smaller cities/towns, the state is doing well; the hot spots are isolated and probably associated with facility outbreaks.  Also, looking at the chance of being exposed in a group of 50 (e.g, eating at a restaurant), almost all of the state is blue or clear, meaning less than a 10% chance of someone else in there being COVID-19 positive (still to high for me, but everyone has different standards).



Regions:

In the spring, COVID-19 in Virginia was primarily a concern in the DC suburbs.  Over a 3-4 weeks, in late may to early June, NOVA recovered, and for about a month, the disease was under control, to the point where the restrictions were eased.  Unfortunately, in eastern VA/Hampton Roads, the easing of restrictions results in a surge in cases,  which peaked around August 1 (and resulted in stricter restrictions in that area).  Since then, the the exception of growth on college campus, the disease has been stable, except for the rural parts of the state, where safeguards are largely ignored.  The trends are clearly visible in the figure below.

With this, we have completed the transition from COVID-19 being an urban disease to being a rural disease.    But, looking at the weekly numbers, it appears that the rural areas, whose caseloads were already increasing, surged with the the influx of a carefree demographic (college students).  Over the last few weeks, that seems to be improving.  We are not out of the woods, but I am far more optimistic than I was even a week ago. 



Regional growth rates are (in fraction per day) continue to to show improvement.


NOVA: .990 -- GMU

Central VA: .981--  VCU

Hampton Roads/Eastern VA:  0.961 -- W&M, CNU & ODU

SW VA:  0.962-- VT & Radford

NW VA:  0.952-- JMU & UVA



The state as a whole is is decreasing with Rt=0.986


The following table shows the number per 100k for each region. Again, NOVA and Eastern VA are doing the best, and NW & SW are doing the worst, but are showing improvements as the college cases are getting somewhat under control -- or at least better than they were.


Daily Cases/100,000 
(corrected for testing)

Region

Last month

Last week

NOVA

 8.8

7.3

Eastern

 9.3

8.1

Central

12.2

9.7

NW

12.9

13.6

SW

17.4

13.2



The following charts are for the 5 regions. in the chart that shows all regions,  The individual line charts show the unfiltered data per day, coupled with the trend lines.  The trend lines show the different periods of growth.    Early in the pandemic, the different parts of Virginia were functioning largely independently, with NOVA mimicking the northern states, and Hampton Roads mimicking the southern states. But, since September 1, the regions have trended with each other.  Note that the nose-dive in the chart today is probably an artifact of the 7-day polynomial filtering I use .








Local/Northern VA:


In the trends of case, we can either describe it as slow growth since late June, or flat since early august.  Both equally describe the data. But, for the last week, we are are 184 cases a day.   What is noteworth




Currently, all jurisdictions are essentially flat.
Fairfax Co.: 0.987
Arlington Co.: 1.006
City of Alexandria: 1.009
Prince William Co.: 0.990
Loudoun Co.: 0.981
The growth rate is defined as Rt, or the growth time constant.  Simply, todays number are approximately the growth rate times yesterday's numbers.  This is the exponential time constant.  Fortunately, the time constants are below 1 and our rate of cases is about 6/100,000 per day.  Ideally, we would be 0, but 6 is much better than our peak in which was around 30/100000K. 


Looking at the trends, since around Sept. 1, there is a clear downward trend in all jurisdictions. The cause of that is unknown, but may relate to the cooler weather.  Alternatively, with school being in session, it could be there is more social distancing.  




What is most noteworthy of the NOVA Zip code map is the the overall lack of contrast.  With the exception of near zero population localities, every part is doing about the same.  There are small scale variations, but the relationships seem to be more related to locations with more shared living arrangements than anything else.  Another way to say this is, while social distancing is hard on all of us, for the lower income people, it may be impossible.





Every part of Northern Virginia is down last week compared with the last month, except for Vienna. The good news is, in the last week, almost all of of Northern VA is showing less than 10/100,000 cases (Alexandria City is the exception).    Vienna, which had a  post-labor day mini-peak, has reverted to its prior status as among the lowest caseload per capita in Northern VA.  I am not sure why the surge occurred, nor do I know why Vienna reverted to its prior status, but I will point out that about 1/2 of my readers are from Vienna, according to google analytics and perhaps changed behaviors :). 

Region

Last month

Last week

Growth rate (%/day)

Fairfax Co

Vienna

 6.7

4.0

-6.2

McLean

 5.4

4.0

-0.9

So. Alexandria

 9.3

9.3

1.3

Reston/Herndon

 8.4

7.3

-2.4

Annandale/Fall Church

 9.3

8.5

-1.4

Fairfax

 6.5

6.8

-0.8

Arlington/Alexandria

No. Arlington

 5.4

5.2

-0.9

So. Arlington

 9.0

8.6

-1.2

Alexandria City

11.8

12.3

1.5


During most of the last 2 months, Vienna and McLean tracked each other, as did Reston and Fairfax.  Except, for labor day to about 1 week ago where Vienna increased its case load.  Now, though, it appears Vienna and McLean are again tracking each other.




Age Distribution: 

As expected, there was an increase in cases among Middle Ages (and young adults) delayed from when the JMU students returned home.  There are about about 150 cases from the JMU students. We are now back to the baseline number for that age group.  The JMU students infected their parents, resulting in an increase of The concern is that the JMU students will infect their families, and we saw an uptick in the middle aged population, which has since recovered; about 50-100 extra people were infected, which was less than I expected.

Note, I will talk about the age distribution in college communities under "college communities"





Colleges

My process combines the VA Department of Health data and what is reported by the colleges.  The report is as of 12:00 ET.   I need to point out that the VDH cases may include cases not affiliated with the university as I am using geographic surveillance.  It is also worth noting that all assume that students feeling ill are going to health service; I have heard anecdotal reports of people not doing that because they did not want to quarantine.  The colleges usually update the dashboards after this post, or on Monday/Tuesdays.  Except for Radford, all weekly updates are complete at this time.  And the numbers are encouraging (except for UVA).

As the process has evolved, it was clear that I needed to show active cases (e.g., last 10 days) in addition to cumulative cases.

Also, I am assuming the colleges are promptly reporting there numbers to the Virginia Department of Health.  As it turns out, W&M is reporting the cases approximately 2 days after updating the dashboard.  It is probably a result of the phasing of the process.

Note: I have been tuning the following table to improve the estimated number of cases (the order of operations has changed a bit).  Also, I am adjusting the pre-student case oad:  to estimate the number of cases from students, I subtract out the average number of cases prior to the student arrivals from the reported cases.  If the numbers are large (UVA, VT, JMU & Radford), the impact is minimal.  This makes it harder, though, to identify cases in more urban settings, like ODU, VCU and CNU.

RED means there is clear evidence for community spread
YELLOW means there may be community spread; still ambiguous
GREEN means no evidence of community spread
BLACK means they went online.

College

% Positive

Cumulative

Last 10 days

Dashboard Cases

% that had COVID***

VDH Cases*

Est

Cases**

VDH Cases*

Est

Cases**

Va Tech

10.3

1288

6084

 269

1036

925*****

17.8

GMU

2.9

0

3

 0

0

45*****

0.0

UVA

10.4

550

1384

 246

535

590*****

5.8

ODU

2.1

40

71

 1

7

62

0.3

JMU

17.5

1498

7220

 261

1131

 1469

34.0

CNU

3.5

0

23

 0

0

17

0.5

UMW

2.9

0

7

 0

0

12*

0.1

Radford

7.6

557

2744

 15

36

409*****

34.6

VCU

3.2

152

292

3

2

241*****

0.9

W&M  

1.18

13

13

3

4

13*****

0.2

    

* estimated from the number of cases in the zip codes associated with the university removing the pre-student arrival case rate

** estimated number of cases is an attempt to normalize for testing limitations. Specifically, I assume at 5% positive, 100% of the cases would be caught. so I normalize it to that value.  If the % positive is very high (>40%) I am likely overestimating the numbers.
*** Dashboard cases are only counted if I can find the dashboard.  In some cases, it is difficult to distinguish positive tests from cases (1 case may have multiple positive tests; that is mostly at VT).  I include active cases if reported, otherwise, I use total cases.
****% population uses the total reported number of students rather than just those on campus; it may be off when the percent positive is above >40%.
***** Old data, not updated for today.
****** Active cases, not total cases

Large Scale Community Spread:

JMU

JMU is online.  The case count continues to rise.  JMU has been fairly transparent with the situation, but could not get ahead of it.  At this point, it is mitigation.  Harrisonburg is still running 20% positive.  They sent the healthy students home (and some sick kids home), and are allowing the positive to stay on campus, which is critical for society as a whole.  It is worth noting that sending the on-campus students home seems to correlate with an increase in cases in that age group in Northern VA, and later by the age group of their parents.   JMU did not require testing prior to arrival on campus.  JMU plans to reintroduce on-campus activities soon -- this time with about 10x the quarantine space and a plan for prevalence testing.  Note that over the last two months, JMU students resulted in about 85% Harrisonburg's COVID-19 cases.

We have seen the prevalence of the virus in Blacksburg increase with the return of the students. Each day, there are 30 and 100 new cases validated.  There could be more, but some people are just assuming they have COVID 19.Virginia Tech tested only on-campus students.  In the last 2 months, VT student cases, as reported in the dashboard, has accounted for 66% of all of Blacksburg cases.  But -- VT is only reported the student health center results,
With the students return, there has been a marked increase in cases.  Week over week, UVA has been increasing by 25% in the case load.  In the last two months, 76% of the case load in Charlottesville.  I expect the numbers to start to drop, probably by the end of next week, as UVA has imposed much stricter restictions on students.

Watch List:

RADFORD 

Radford was moved to the watch list, as there percent positive has improved.  While it is not how many students at Radford contracted COVID-19.  It would not surprise me to see enough that the community, when isolated effectively has herd immunity (meaning over 60-80% contracted COVID-19).  The only way to know would be antibody studies.  Hopefully, VDH will look into that.  But, currently, it seems that Radford has a manageable number of cases.  While only 57% of the cases in the last two months are attributed to students, there were so few cases prior to the students return, this means either the dashboard is undercounting, or there were a lot of non-students infected by students. 

Other schools:

William & Mary -- so far so good -- No evidence of community spread. They now have a reportable number of cases, with the dashboard showing 13 total cases as of yesterday, up from 10 on thurs, and less than 10 on Wed.  That means since Thursday, there should be at least 4 cases from W&M in either the zip codes or Williamsburg.  The VDH numbers shows 4 cases in Williamsburg and the zipcode.  This came in two days after the dashboard was updated, and probably indicates that 1) W&M is quick to update the dashboard, and 2) there is a process to update VDH.  The good news is W&M confirmed this is the situation.

W&M tested all students prior to arrival in town. Williamsburg is a case where the town/tourists are a bigger threat to the college, than the college is to the town.  Over the last two months, only 16% of the cases were from W&M students, but the students are 40% of the town population.

VCU seems to have the virus under control -- They have beaten back an outbreak, the % positive is good, and there are few new cases. It was promoted from RED to YELLOW. and now Green.  The numbers have shown no significant increase in the last several days; quarantine and isolation space is becoming more prevalent.   Being in an urban setting the zip-code and regional surveillance that works well at some of the other schools is not particularly helpful here.  So, I have to rely on the dashboard.   

CNU -- Students have been back upwards 1 month. A few cases.  Under control.

ODU -- Nothing noteworthy.  My concern with ODU is they did not test the students, so there may be asymptomatic/presymptomatic spreaders on campus (see JMU). Yesterday, they updated the dashboard to show 59 cases on campus, which is about what I would expect based on non-tested students.  But the dashboard has not been updated since Sunday. They update it once per week.  We will see if they infected other students.  

UMW -- Nothing noteworthy.  A few cases but they just returned.  I am concerned because they did not test all students.

GMU -- Nothing noteworthy.  GMU tested all students.

College Communities:

When I started talking about communities, the  focus was on the safety for incoming students.  Unfortunately, that concept as changed.  Now, we are seeing the colleges impacting the surrounding communities.  If we look at the age distribution of cases in the communities of JMU, Radford and VT (New River, and Central Shenandoah health districts), we see that, starting about 2 week sago, number of cases for non-college age citizens is increasing -- about two weeks behind the college age curve.  This suggests the disease is infecting the general population.  So far, it looks like about an extra 100 seniors were infected; tha thas resulted in a few extra deaths.  This is the concern.  This trend has been observed elsewhere in the country, where the college students infect the more vulnerable populations.





Commentary:


Attribution:

1) You can repost / share in the entirety by forwarding the link, 2) If you want share partial content, you must receive my permission – I need to make sure you understand what I am saying. If anyone sees this work being used without attribution, please let me know as soon as possible. I am willing to have an informed discussion / debate on my approach, but I want to make sure the proper context is captured.


Links: 

Source data is from the Virginia Dept of Health COVID Site

Why I did this:  About the blog
I have thoughts on the spread in college communities which can be seen here.  This is the same link at the top of the write-up.

Other Sites:  John's Hopkins

Kids can pass covid to parents: Pediatric SARS-CoV-2: Clinical Presentation, Infectivity, and Immune Responses




A fun video showing masks work, guy style:




How to wear a mask.

Politics:  Some lie.


Donald Trump yesterday said that without blue states, the death rate would be much better.  He needs to stop using alternate facts.  Red and blue are defined by who the state voted for in 2016.  47% of the deaths come from red states, which is about his percent of the popular vote.  But, more importantly, after June first, when states could use science to mitigate the virus, 65% of the deaths are from red states.  Facts matter.




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